Good-Bye
by TricksterAngel1
Summary: The Doctor goes on his good-bye tour and ends up getting into a situation with the Avengers and S.H.I.E.L.D. Maybe he should have tried to stay out of New York more, but something big is lurking in the shadows waiting for the Doctor. Will he make it out of this encounter intact?
1. Prologue

**Disclaimer: In case this FanFic seems really familiar to any of you, yes I have permission to use parts of hiholly123's story "Only the Beginning". So don't report me for something I have already asked permission for. Thanks. I don't own Doctor Who or Avengers.**

 **WARNING: May contain some language and other things not suitable for people 13 or younger.**

 **Prologue** **:**

I had left my brilliant Ponds. I had said good-bye to Craig, but more importantly, I had _left_ my Ponds. I sighed and stroked the console hearing a hum of comfort.

"Thank you Sexy," I said, smiling sadly.

She hummed again and flashed the lights softly. I sigh again and lean against the console. Thinking back to all of the adventures I had with my Ponds and all of my other companions, I smile sadly, thinking about all of my failed attempts to protect them. I felt something drip on my hand and looked down. To my surprise, I was crying. I laughed bitterly and wiped the tears away. My thoughts then drifted to my last face and the events leading to my regeneration into this face.

I was forcefully thrown from my dark thoughts when the console room suddenly tilted sideways. I was thrown around the room like a rag doll and slammed hard into the railing. The air leaving my body in a whoosh of air. I gasped for breath and was then thrown again, this time hitting my head on the edge of the console knocking me unconscious.

 ***TIME SKIP***

I woke up approximately three hours, forty-three minutes and twelve seconds later and found the TARDIS silent and dark, only the backup generators were on. Trying to sit up, I fell back down with a sharp cry of pain as my ribs and head immediately protested my movement. I lay still taking stock of my injuries, which included three broken ribs, a concussion and a stress fracture in my left ankle. After finally getting my breathing under control, I sat up slowly wincing in pain the whole way.

Slowly, I became aware of people shouting something through the TARDIS door. Crawling toward the door, my vision tilted making me nauseous. Finally, I made it to the door and pulled myself into a standing position, making sure that I didn't put too much pressure on my fractured ankle. I swayed dangerously, tilting to the side my hand shot out for balance. I winced, my head throbbing along with my heartbeats and the pounding on the door. I pulled myself up from my slouched position, fixed my bow tie and plastered the most fake smile on my face and then opened the door.

When you hear an ominous clicking noise it's safe to say that you are in a lot of trouble, especially when that clicking noise is of the safety's being turned off on guns. I slowly raised my hands in the universal sign for surrender and stepped the rest of the way out of the TARDIS. The first thing I noticed were four guns pointed in my direction. The second thing I notice is that I seemed to have landed on a ship of some sort.

"Who are you?" a gruff voice demanded.

I turned to look at who spoke and I saw a dark-skinned man who looked like a pirate. I smiled and said, "Just someone traveling through. I mean no harm, so if I'll be on my way- " I tried to move back into my ship, but the guns clicked again, signaling that they were not going to let me go so easily.

"I'll only ask this once more," the pirate said, "Who are you?"

I sighed, but then winced slightly when a sharp pain shoots through my ribs.

"I'm the Doctor," I said.

"Doctor who?" another man asked. He was standing slightly behind the pirate and wearing a suit that reminded me of one of the guys on the movie MIB.

I grimaced at that, remembering everyone who ever said that to me.

The pirate looked at MIB guy and nodded. That must have been a signal because he and two others stepped forward cautiously, guns still pointing at me and when they came within reaching distance, the two others put their guns in their holsters and reached forward and grabbed my arms, putting them into some kind of handcuffs behind my back.

The jerking motion of my arms being forced behind my back caused my ribs to protest loudly. I hissed loudly in pain. Dark spots filled my eyes and I blinked rapidly, trying to push the spots away.

The guards hesitated for a brief moment, but they then just continued on like nothing had happened. They practically dragged me to a room that had some sort of glass cage in the middle of the room. I stumbled and was roughly pushed inside, I instantly fell to the floor from the momentum. I cursed loudly in Gallifreyan as my ribs met the metal floor.

Pirate man looked at me stoically while MIB guy and another man with a bow looked at me with hidden sympathy. I didn't care, I was too busy trying not to let the pain drag me under. My breathing was very heavy and I could barely breathe, the darkness in my vision threatened to pull me under but I fought it back. For now, at least.

I stood up slowly, gritting my teeth, with my hand wrapped around my ribs and my eyes squeezed shut tightly in pain. The pirate who was now the only one left out of the three, watched me as I stood, his one eye not leaving me. He just stood there with his arms crossed. Standing up straight, I kept my weight off of my ankle and stood there, hunched over slightly.

"Sooo…. Is this going to be an interrogation?" I asked with as much bravado as I could muster. Which at this point was not a lot. "Because if so, this is the worst one I have experienced so far, and I've been in a lot of interrogation's."

"This is not an interrogation. Well, at least it won't be if you answer my questions," pirate said.

"I'm sorry, I'm afraid I don't know who you are or where I am," I said as politely as I could while still trying to not pass out.

"I am Nick Fury, Director of S.H.I.E.L.D. You are on our Helicarrier, and since I'm assuming you're some kind of alien life form, seeing as you arrived in some kind of ship, you are on planet Earth," he said, like he had this type of conversation all the time.

"I always have to end up on Earth don't I," I said quietly to myself.

"What are you and where do you come from?" Fury snapped impatiently.

I laughed bitterly and said, "I am a Time Lord from the planet Gallifrey."

"Are there any more of you out there that I should be concerned about?" he demanded.

As soon as he asked that question, my mind flashed back to the days of the Time War and how everyone had died and how there was no other choice but to destroy my home planet and the Daleks along with it.

"No. There is no one else out there. I am the last of my kind," I said, pain coating my voice.

Before Fury could ask any more questions, MIB guy came back into the room and whispered something in his ear. Fury nodded and said, "Bring them up and call Thor while you're at it."

MIB guy nodded and left. I then realized what Fury had said and I started panicking. The last time I saw Thor had been right after I ended the Time War, and he had been so furious at me, that he had tried to kill me.

"I'm sorry, did you just say Thor?" I asked shakily. My vision was starting to turn dark.

Fury just looked at me confused and he didn't answer. My breathing picked up and the pain became too much for me to handle. I then fell onto the floor and I heard someone shouting something. The darkness then swallowed me whole and I drifted away.

 **To be continued…**

 **A/N: Hope you guys liked the first chapter. I will hopefully update once a week for you guys. Please review it helps me out, just don't be mean about it. Constructive criticism only. Thanks.**


	2. Chapter 1

**Disclaimer: If I owned either they would have been completely different.**

 **WARNING: May be a bit OOC for some characters, maybe all. I don't know yet.**

 **A/N: I am so, so sorry that this has taken me a while to update. I just started college last week so there will be delays with getting the chapters out there. Hope you enjoy!**

 **Chapter 1**

I awoke to the sound of a familiar beeping noise. The sound of the beeping seemed to be getting louder and it started to take shape into one sound that I never wanted to hear again.

 _Beep-beep-beep-beep, beep-beep-beep-beep, beep-beep-beep-beep, beep-beep-beep-beep._

My eyes snapped open and I tried to get up but found that I couldn't. I looked around wildly, and then noticed that I was lying on a hospital bed. Trying to sit up, I noticed that my ribs were wrapped and my ankle was elevated, but the four beat beeping caught my attention again and my breathing picked up its pace, and thoughts started racing around my head.

' _He can't be here, he's dead! How is he doing this?!'_

I was so caught up in my thoughts, that I missed the door opening and someone entering the room.

Suddenly, I heard someone talking to me and I strained to hear what they were saying. I focused harder and realized that whoever was with me was trying to calm me down.

Finally, managed to calm down enough that I could hear again. My eyes open and I look around the room. I notice that there is a heart monitor machine next to the bed that I was lying on, and my face colored in embarrassment.

' _I can't believe I panicked over hearing my hearts beat.'_

I hung my head and hid my face in my hands embarrassed but relieved at the same time. Relieved because that meant that _**he**_ wasn't here.

Someone cleared their throat and I uncovered my face and looked up. The culprit was Fury, he was glaring at me, he looked pissed. I just stared calmly back at him not even close to be intimidated. I've faced down foes who were more intimidating than him pretty much every day of my lives. We stared at each other for a minute trying to make the other look away first. I ended up looking away first after I shifted, wincing slightly, as fresh waves of pain rolled through my body.

Coughing awkwardly, I turned back to Fury and asked, "Where am I?"

"You are in our infirmary. Figured it would be easier to take you here instead of trying to treat you in your cell," he deadpanned.

Before I could say anything more, the door to the infirmary swished open and five people stepped into the room.

"- I think this would be an excellent opportunity to-," the one with the weird beard thing was cut off abruptly by the man with glasses elbowing his side.

The beard guy looked indignant and opened his mouth, but the big blonde guy gave him a look and he quickly shut his mouth and crossed his arms, pouting slightly.

The other two people were standing slightly behind Fury and they were odd, but not as odd as the three men. The woman was dangerous looking and I made a mental note not to get on her bad side, ever. The man was kind of strange, he was carrying a bow and had a quiver full of arrows strapped to his back. Both of them gave off the vibes of ' _Don't fuck with me.'_

My observations were interrupted when the man with glasses came over and asked, concerned, "What happened to you to get these types of injuries?"

I looked at him for a second, surprised that he would even care, so I just shrugged and cheerfully said, "I was just coming back from this _lovely_ planet and my ship went haywire, then I landed here, and then pirate over here put me in a glass cell and now I'm here."

He watched me for a minute and looked as if he couldn't decide if I was lying or not. I smiled, amused at his reaction, not like I don't get that kind of reaction enough. I am apparently someone who people can't take seriously, not that I blame them. This regeneration is a bit on the childish end.

"Well, now that we have that all settled, can we get back to the task at hand?" Fury asked everyone sarcastically.

Everyone looked at the ground awkwardly, feeling like a child who had just been scolded after doing something bad.

Fury looked at me, crossed his arms over his chest and said, "So, you mind telling me what you are doing here?"

I looked at him for a minute and thought the question over. I of course had no idea why I was here or why the TARDIS decided to send me here, rather violently, might I add.

I plastered a smile on my face and said cheerfully, "Nope. Not a clue. Although if I knew how to get out of here I would, but at the moment my ship is a bit on the damaged side, so that isn't going to be possible at the moment."

He glared at me suspiciously, I just smiled my fakest smile and started fiddling with my hand, like I normally did when I get nervous, or I guess, in general.

Before Fury could say anything more, the room darkened and there was blasts of thunder and lightning. I cringed, immediately knowing that this was not going to end well. The storm continued for a second and then I could hear a loud pounding of someone's boots on the floor heading towards the infirmary. I sighed and felt resigned to the fate that was about to befall me.

There was a fist pounding on the infirmary door, and I heard the one person that I had hoped to never hear from again, murderously yelling, " **DOCTOR!"**

 **A/N: Sorry for the cliffhanger. NOT. These cliffies won't happen all the time, but I can't guarantee that they will not happen. Please drop a review it will help out a lot. Thanks!**


	3. Chapter 2

**Disclaimer: Still don't own.**

 **A/N: Sorry this is so late guys! I have been really busy at school so I won't always be able to update every week, but I will definitely try.**

 **Chapter 2**

I shrunk down as much as I could on the infirmary's bed, but I knew that it would be useless. Thor would get in here one way or another. I looked around for any possible exits, but of course the only exit was the door that Thor was currently at.

"YOU CAN'T HIDE FOREVER DOCTOR! COME OUT YOU COWARD!" Thor shouted through the door.

I shivered and looked at Fury, "You might as well let him in before you have a broken door."

He nodded at the guards by the door and they opened the door.

What happened next was so fast that my head spun. The door had opened and a red and silver streak had practically flown across the room towards me. I felt myself being lifted and I was roughly slammed into the wall next to the bed. I coughed violently and felt something trickle down my chin, but I was too busy concentrating on the enraged being with his big hand wrapped around my neck.

Thor's eyes were filled with rage and he looked as if he would kill me at any time. My hands instinctively came up and tried to take the pressure off of my neck, but his grip was too tight.

I coughed again and more liquid- which I now realize was blood- was trickling down my chin at an alarming rate.

I looked up at Thor, smiling sadly and barely managed to choke out, "Hello Thor, long time no see. You've grown."

Of course that just pissed him off even more and he roughly slammed me against the wall. This time my head slammed into it and my vision swam dangerously. I closed my eyes and tried to keep my breathing under control.

Next thing I know, I'm on the floor and greedily taking in the air. I coughed and wiped my mouth and looked down at my hand. Blood.

' _That's not good,'_ I thought to myself dazedly.

I looked around and saw that a gold and red suit, and the two blonde men were now holding Thor back and yelling at him to calm down. Thinking about what to do next, I reached up and grabbed the edge of the bed and tried to stand, tried being the key word. I managed to get to get halfway up before the world suddenly tilted sideways and I fell back down with a thud.

That, of course drew the attention of everyone in the room. I looked at them sheepishly and waved my hand at them.

"Sorry 'bout that, just fell," I said nervously.

Thor ripped his arms away from the three men and looked at me with cold eyes. he then turned to Fury and said, "You should not have him anywhere where he can use something to escape. I would put him in that glass cage you have."

Shockingly enough I wasn't surprised that he would say that, but of course, I had to open my big fat mouth.

"Is that anyway to treat your uncle, Thor?" I asked in a light tone.

Thor snarled and made to move towards me, but thankfully he was blocked from doing so.

"You stopped being my uncle when you left and killed all of your people!" He said, his voice filled with ice and fury.

I flinched and tears sprang to my eyes. The war. That was all I could think about. The sky burning, people screaming in agony and suffering. People fighting until they were the last one standing and then they would eventually be cut down. People who tried to save their families, only to watch them die right in front of them with one word that everyone fears.

"Thor, do not presume to know what happened in the war when you were not there to witness the atrocities that happened," I said in a low voice that was filled with emotion.

He sneered at me and crossed his arms, his stance screaming, 'why should I even believe you?'

During our discussion, well more like fight, everyone in the room had been watching us. Their heads moving between the two of us, like they were watching a tennis match. When Thor had said that I killed my people, their faces tightened in hidden fury and hatred.

"I'm sorry, did Point break just say that you killed your people? How could you do that?" The red and gold suit said, anger dripping in his words.

I looked at him and said coldly, "I think that is none of your business."

"Well, I think we have a long discussion ahead of us, but first we need to get you to your new accommodations," Fury said, his face closed off.

I turned to face him, "Well in order to get this show on the road, I need a bit of help getting off of the floor."

Fury looked at the two guards and gestured to me. They came over and roughly pulled me up from the floor. I bit my lower lip hard so as not to cry out in pain. Fresh blood ran down my chin from biting my lip.

They forcefully dragged me out of the room and down the corridor. We were walking for what seemed like forever, before we finally got to wherever we were going. The room was huge, it had a glass cage in the middle of the room and it was big enough to fit at least fifteen people comfortably.

"Is this going to be my new room?" I asked sarcastically.

The only response I got was the guards pushing me into the cage. I fell roughly on my knees, jarring my broken ribs and starting a new round of coughing and blood.

I crawled to one side of the cage and leaned against the glass, looking out at the people around the cage.

"So… what now?" I asked.

"Now, you give us answers. Thor here says you're dangerous," Fury said, "I just want to know what you are doing here and why he thinks that you are dangerous."

Thor looked at him and said, "His people were in a war with a formidable race and they were winning, _he_ then blows up the entire planet in revenge for the war ever happening."

I scoffed loudly, drawing everyone's attention.

"Do you honestly believe that Thor? After everything that I have done for you, you believe some lie over the truth that I gave you all those years ago?" I asked, disappointed that he wouldn't believe me after everything.

"Yes, I do believe that. I also believe that you are a cold-hearted murderer who doesn't care for others," Thor spat.

I looked down at my lap and tried to keep the tears at bay, "If that is what you believe-"

"That _is_ what I believe," he said with conviction.

"Then you are a fool. A fool who believes everything he is told and does not listen to others who are telling the truth," I said softly, still not looking up.

"I AM NOT A FOOL! I KNOW THE TRUTH!" He roared.

I looked up at him, "Do you really though?"

My hearts were twisting painfully in my chest. I could hear them cracking under all of the memories of the Last Great Time War. Looking Thor in the eyes I said, "You weren't even there, so how would you know what happened?"

"I know enough," he said gruffly.

I closed my eyes and blocked everything out. I didn't want to talk to anyone right now, so I let myself fall into unconsciousness and hopefully when I awoke, I would be mostly healed.

If only I knew.

 **A/N: And that's a wrap! Guys please review I don't really know if anyone actually likes this or not and it would be great to know if I was doing anything right. So please review! Thanks.**


	4. Chapter 3

**Disclaimer: Don't own. So don't come after me.**

 **A/N: I'm so sorry guys! I feel so bad about not updating this story sooner. I got so caught up in college and having some mental issues. Here is the new chapter I hope to have the next one up sooner than this one. Thank you all for sticking with me!**

 **Chapter 3**

I woke to the sound of someone shuffling around outside my glass cell. Opening my eyes, I saw Thor with his hammer in his hand and a scowl on his face. Shifting slightly so as not to draw his attention, I gasped loudly in surprise and grasped my ribs in agony. I was shocked, my injuries should have healed by now, especially after having slept for a while.

After the pain subsides a bit, I looked up and noticed that Thor wasn't alone anymore. There were seven other people who I had seen before, standing with him; Fury, the one with the armored metal suit, MIB man, the redheaded deadly looking woman, the man dressed as an American flag, the man with a beautiful compound bow, and the man with glasses who looked nervous. They all looked at me with varying expressions, or no expression with some.

"Do you need something?" I gasped out sarcastically, my breathing still labored.

Thor took a step forward and glared at me, "You are a threat to everyone on this planet, so man of Fury has agreed to keeping you locked up in this cell until I have decided what to do with you," he said sharply.

I stared sadly at him, "Oh Thor, what happened to that happy little boy who held no anger?" I asked quietly.

Snarling loudly, Thor stomped up to the cell and stood in front of it. "You have no right to ask that since you killed my friend when you destroyed Gallifrey!" He thundered.

I froze. His friend, oh Rassilon! It had been so long since I had seen Thor last that I forgot I had brought someone with me every time I had visited Asgard. How could I forget that?! The blood drained from my face as I continued to remember what had happened to them. Of course, not how Thor thinks. They actually died much later, a lot later, long after the Time War ended.

Lost in my thoughts of a time long past where there was no hope, I didn't notice that the eight individuals standing before me who had varying expressions of curiosity on their faces, except of course for Thor. He was glaring at me with such hatred on his face, that my hearts clenched in pain at the knowledge of having lost him.

Changing the subject quickly, I stared at Thor, swallowing nervously I asked the one question that had been on my mind since I first saw Thor in the infirmary.

"Where's Loki?"

Thor stiffened and his face darkened considerably. Absently, I noticed that the others behind him had also stiffened.

Completely uncomfortable now, I shifted a little and then realized that that was not a good idea right now because pain swept through me and I let out a soft hiss of pain, hoping that they didn't hear me. Unfortunately for me, everyone heard.

Instead of answering my earlier question, Thor frowned at me, concern flashing over his features for a second before it settled into a mask of indifference.

"You should be healed by now," Thor states emotionlessly.

"I noticed," I said bitterly. "I seem to not be able to heal as I should and I have no idea why."

Thor's face remained impassive throughout my explanation, but the people behind him just looked confused.

Sighing slightly, I took pity on them and started to explain why this was bad to them, "My people had a faster healing ability than humans, we also have a neat trick to cheat death with. It's called regeneration, we can change everything about ourselves starting with our cells. When our cells start to die, most of us decide to keep living and then the process starts. Golden light explodes from our bodies and we then change. Hair, gender, body type, voice, height, everything.

"Most of you? What do you mean by that?" the man with the gold and red suit asked.

I looked down sadly, not liking where this was going. "It's exactly as I said, some of us didn't want to continue on anymore so they died. Not that I can blame them."

"What do you mean?" Thor questioned.

"The Time War!" I shouted back at him, finally fed up with the questions. "In the Time War, many fought in the beginning, we were proud to be fighting and we learned to love it." I was panting now, anger and sadness coursing through me. "But later, most of us wanted out, and the only way of doing that was by jumping in front of our enemy and hoping that they would shoot us instead of capturing us. The rest were consumed with the war. There was so much blood on our hands, and we loved it, craved it, and it drove us mad."

"Which were you?" Fury asked, arms crossed but his body was tense as if ready for an attack.

I could feel my hearts sink in my chest, this was definitely not something I wanted to talk about, so I did what I always do in these situations. I changed the subject.

"I had a friend once, Thor knows him. He and I went to the Academy together and we were very close," I said softly. "Something happened to him when we were eight years old, and it changed him. After, that, he became obsessed with becoming better, more powerful. I tried to stop him but he just laughed at me and said, 'Come now Doctor, you really think that _you_ of all people can stop me?' He was right, I couldn't stop him and people were hurt because of me." Sighing sadly, I forced myself to continue. "Later on in our lives he would have bouts of sanity and we would travel together until he became mad and power hungry again. I took him to all the places we had wanted to go as children. Including Asgard," I said, looking directly at Thor.

Thor's impassive face had melted into a look of nostalgia as my story came to an end. Suddenly, the nostalgia changed into burning rage.

"You cannot and will not change my mind about your imprisonment! I refuse to accept your lies, trickster!" Thor roared, slamming a fist against the glass causing it to crack.

I looked at the glass uneasily, hoping beyond hope that the glass wouldn't shatter.

"They are not lies Thor. Why can't you see that everything I've ever told you was true?" I asked softly, looking at him.

Before Thor could answer my question, a loud noise comes over all of the speakers in the room.

 _ **Tap-tap-tap-tap, tap-tap-tap-tap**_

My face automatically paled, my body started to shake, and my breathing picked up. Eyes darting around the room, I found that Fury was shouting into his earpiece and the others were starting to get into defensive positions.

"What did you do?!" Thor shouted at me over the loud tapping noise.

Trying and failing to speak, I just looked at him with fear in my eyes and hearts.

"He can't be here, he can't _be_ here, he can't. I watched him die," I heard myself whisper desperately, black spots littering my vision once more.

Closing my eyes, I started trying to slow my breathing down. After a while, I felt confident that I wouldn't pass out again. I jumped a little and my eyes snapped open when Thor started yelling again.

"Who? Who is doing this?!" Thor shouted angrily.

The tapping suddenly cut off and I knew that _he_ truly was back. I could feel it in my bones.

"The Master," I managed to say shakily, still frozen in place, terrified of what was to come.

 **A/N: The cliffies are fantastic, right?! Not for you obviously, but who cares! .**


	5. Chapter 4

**Disclaimer: Do you see Tony Stark dating Loki? No? Then I don't own them.**

 **A/N: I am so sorry guys! I really have been trying to get this chapter hammered out but it doesn't seem to be cooperating with me. Am I moving the story along to fast? Please let me know if I am and I will try to slow it down for you all. Review anyway though so I can get some good feedback from you all.**

 **Chapter 4**

Thor froze, many emotions flickering across his face. Surprise, confusion, melancholy, anger and then a burning rage that I had only ever seen on _ **his**_ face.

"Lies! He is dead! You killed him yourself!" Thor roared.

I stared at him in disbelief, unable to understand why he thought that _I_ had killed him, when it was _**him**_ who had almost killed me hundreds of times.

"Is that what _**they**_ told you? I can't believe that you would believe _**them**_ over me, your own Uncle. I don't think you understand what actually happened Thor. I am very disappointed with you right now." By the end of my speech, I had deflated and felt an overwhelming bitterness towards Thor and the Gallifrey High Command. Who had always twisted everything that was said about me and what I do.

"You are not my Uncle as you are not related to me," Thor spat venomously.

His words hit me like a punch to the gut. All of the air whooshed out of my lungs as I remembered all that I had lost. Embarrassingly, my eyes started to water as I gazed sadly at Thor.

"Never in all of my years of living have I heard something so ridiculous," I said. "Family doesn't ever end with blood Thor. I hope you will always remember that."

Thor scoffed, turned toward the door and stormed out of the room. Everyone else just stood there silently. Unsure as to what they should do now.

"Well, this is awkward," the man in the red and gold metal suit drawled out.

Flag man just looked disapprovingly at the metal man, like he was hoping that showing his disapproval would make the other man sorry for his outburst.

 _'Yeah right, as if.'_

Ignoring the metal man's outburst, Fury looked at the others and then swept out of the room with a dramatic flutter of his trench coat. Seconds later, everyone still left outside of my cell looked at each other, a silent conversation happening between them. If I wasn't locked in a glass cell I would be very amused, but sadly that was the case.

Suddenly, an annoyed huff escaped the man dressed as the American flag. The other four people looked at him sheepishly and then practically raced out of the room. Except of course for the redhead. She walked out slowly, with all the dignity and grace of a cat being told off for trying to eat the pet mouse.

Alone with the flag man, I suddenly got really nervous. And when I get nervous, I do what I do best. Talk.

"I'm sorry, I don't know your name. I don't want to keep calling you 'the man dressed as the American flag' in my head," I rambled slightly.

The man looked a little amused and then said, "I guess I can tell you my name. I'm Steve Rogers."

"Hello Steve Rogers! I'm the Doctor! Well. I guess you already knew that," I said, highly embarrassed by the end of it.

Steve looked semi amused but then his expression went serious.

"How could you kill your own people?" Steve questioned with a look of disgust and sadness on his face.

Once again, the air whooshed out of my lungs. Deciding that the floor is going to become uncomfortable for this topic, I slowly stood up, wincing the whole way and walked to the little bench. I sat on it slowly and leaned back against the glass to keep the pressure off of my injuries.

Looking at Steve again, I quickly analyzed the situation. If he was asking me these kinds of questions that meant that someone was listening in or watching what was going on. Probably both in this case.

Taking a breath, I started to talk. "I did what I had to do in order to protect everyone in the universe."

"What do you mean by that?" He asked.

"Exactly what I said. The Daleks had already destroyed most of Gallifrey and had taken the Citadel within the first fifty years of the war. I had led the Fifth Time Lord Battle Fleet against the Daleks in the Tantalus Eye for almost a hundred years, and we lost. Every single Time Lord that had been in that fleet either died from the Daleks or by their own hands by the end of the battle. Except me." Pausing here, I tried to keep the memories of those hundred years at bay but it was a losing battle. If I wasn't careful I would slip into my memories and possibly never resurface.

"After those hundred years of fighting, I finally woke up and looked around like it was the first time I had seen the war. I told myself 'No More' and I fought back against the few Time Lords and Daleks alike that were still around after four hundred years. I took 'The Moment', which is essentially a planet eater, and ran. I set it up in a barn on Gallifrey and I activated it. I had planned on still being on the planet when 'The Moment' went off, but something told me I was still needed. So I got on my TARDIS, the blue police box, and ran away."

I stopped myself there because I didn't want to tell them anymore about what had happened during those four hundred years of blood and carnage, and because I was hoping he would skim over that I didn't tell him everything.

Of course, my luck is just terrible these days.

Steve looked at me for a second and then asked the one question that pushed me over the edge and with it the last of my remaining barriers of the Time War.

"What happened during those years that you fought in the Time War?"

With those words being spoken, the memories hit me like a tidal wave, and I was pushed under the depths into the black unknown.

 **A/N: Please! I beg of you! Review! Also, whoever can correctly guess what the reference I made is and where it's from can give me some plot ideas I can use later!**


	6. Chapter 5

**Disclaimer: Don't own.**

 **A/N: Well… let's see how this chapter ends up. I don't have anything prewritten at this point or any point in the future so we'll see where the story leads.**

 **Chapter 5**

Bridge Surveillance Table POV

After Thor and Fury had stormed out of the glass cell room, it was decided between the rest of the Avengers who would stay and talk to the alien. The fast paced "conversation" (aka, body language and dirty looks) took about thirty seconds to decide. Steve huffed out a half amused half annoyed huff and the rest of the members looked sheepishly at their fearless leader.

The rest of the team took off quickly to the bridge to watch the show. While some were full out sprinting (Tony and Clint), others were restraining the urge to run like the others (Natasha and Bruce). Getting to the bridge in record time, the team practically raced to the surveillance table where Fury, Coulson and Thor were already there waiting for them.

"Did we miss anything?" Tony asked, panting.

"No. Now shut up and sit down, Steve is about to start questioning him," Fury growled, folding his arms over his chest.

The team and Thor all sat down around the table and settled in to hear what was happening.

 _'-_ _I'm sorry, I don't know your name. I don't want to keep calling you 'the man dressed as the American flag' in my head.'_

Tony snickered loudly at that, having been trying to come up with some better names for the Captain.

' _I guess I can tell you my name. I'm Steve Rogers.'_

' _Hello Steve Rogers! I'm the Doctor! Well. I guess you already knew that.'_

Several chuckles rang out around the table at that. Thor on the other hand, scowled angrily, as if remembering times past.

"Get to questioning him Captain," came Fury's cool voice from across the table.

Around the table, some looked confused for a second before understanding hit them. Steve had a com on him.

 _'How could you kill your own people?'_ Steve finally asked.

Silence fell over the bridge as many of the personnel stopped what they were doing and listened to what was going on.

At the table, the Avengers and Fury (even though you couldn't tell) leaned forward to hear what the reply was. There was complete silence as they watched the alien slowly and painfully get up off of the floor and make his way to the bench, where he sat down and leaned against the glass wall. The alien was silent for another minute or so before he took a deep breath.

 _'I did what I had to do in order to protect everyone in the universe.'_

That reply was something that through everyone off. They were not expecting an answer like this.

Suddenly, the sound of something cracking came from Thor's direction and everyone turned to find him looking at the screen murderously and the arm of the chair he was sitting in cracked. Everyone wisely said nothing about it in order not draw attention to themselves. They did not want an angry god coming after them.

' _What do you mean by that?'_ Came Steve's voice, grabbing everyone's attention once more.

 _'Exactly what I said. The Daleks had already destroyed most of Gallifrey and had taken the Citadel within the first fifty years of the war. I had led the Fifth Time Lord Battle Fleet against the Daleks in the Tantalus Eye for almost a hundred years, and we lost. Every single Time Lord that had been in that fleet either died from the Daleks or by their own hands by the end of the battle. Except me.'_

There was a pause here, like he was trying not to remember something. The team leaned forward more to see the emotions that were running rampant on the aliens unguarded face.

 _'After those hundred years of fighting, I finally woke up and looked around like it was the first time I had seen the war. I told myself 'No More' and I fought back against the few Time Lords and Daleks alike that were still around after four hundred years. I took 'The Moment', which is essentially a planet eater, and ran. I set it up in a barn on Gallifrey and I activated it. I had planned on still being on the planet when 'The Moment' went off, but something told me I was still needed. So I got on my TARDIS, the blue police box, and ran away.'_

There was another pause here but this time it was longer. Long enough for Thor to slam his fist onto the table and the rest of the team to contemplate what was said.

"That coward! He should have stayed there! His people needed him and he just-" here, Thor's voice trailed off as if his mind was waging war with itself.

Bruce, who had been watching what was going on said, "Something doesn't feel right."

"What do you mean?" said Natasha, silently agreeing in her head that something big was going to happen.

"I mean that this Doctor keeps cutting himself off when he gets to a certain part of his story, like there's something more to it than he's saying," Bruce replied, putting his glasses on and leaning in to get a better look at the Doctor's face.

Silence fell over the table as the team contemplated this ominous statement.

When Steve opened his mouth to ask his next question, Bruce suddenly found something of value and with a terrified expression on his face, yelled, "No, no! Steve stop!"

But it was too late.

"What happened during those years that you fought in the Time War?"

 **A/N: Sorry that this chapter was a little shorter than the others, but I promise that the next one will be longer. Ta ta for now! Please drop a review letting me know how I'm doing!**


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